Published online 10 November 2017 Nucleic Acids Research, 2018, Vol. 46, Database issue D661–D667 doi: 10.1093/nar/gkx1064 WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research Denise N. Slenter1, Martina Kutmon1,2, Kristina Hanspers3, Anders Riutta3, Jacob Windsor1, Nuno Nunes1, Jonathan Melius´ 1, Elisa Cirillo1, Susan L. Coort1, Daniela Digles4, Friederike Ehrhart1, Pieter Giesbertz5, Marianthi Kalafati1,2, Marvin Martens1, Ryan Miller1, Kozo Nishida6, Linda Rieswijk7, Andra Waagmeester1,8, Lars M.T. Eijssen1,9, Chris T. Evelo1,2, Alexander R. Pico3 and Egon L. Willighagen1,*
1Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands, 2Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands, 3Gladstone Institutes, San Francisco, California, CA 94158, USA, 4University of Vienna, Department of Pharmaceutical Chemistry, 1090 Vienna, Austria, 5Chair of Nutritional Physiology, Technische Universitat¨ Munchen,¨ 85350 Freising, Germany, 6Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Suita, Osaka 565-0874, Japan, 7Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA, 8Micelio, Antwerp, Belgium and 9School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, 6229 ER Maastricht, The Netherlands
Received September 14, 2017; Revised October 09, 2017; Editorial Decision October 10, 2017; Accepted October 25, 2017
ABSTRACT omics data. New search options, monthly downloads, more links to metabolite databases, and new portals WikiPathways (wikipathways.org) captures the col- make pathway knowledge more effortlessly accessi- lective knowledge represented in biological path- ble to individual researchers and research communi- ways. By providing a database in a curated, ma- ties. chine readable way, omics data analysis and visu- alization is enabled. WikiPathways and other path- way databases are used to analyze experimental data INTRODUCTION by research groups in many fields. Due to the open and collaborative nature of the WikiPathways plat- The WikiPathways initiative (wikipathways.org)startedin 2008, creating a platform where pathway curation could form, our content keeps growing and is getting more be performed by means of crowd sourcing (1). The plat- accurate, making WikiPathways a reliable and rich form’s knowledge-base supports many life sciences com- pathway database. Previously, however, the focus munities, ranging from plant biology (2) to drug discov- was primarily on genes and proteins, leaving many ery (3). The use of pathway knowledge in the life sciences metabolites with only limited annotation. Recent cu- is wide-spread, supported by many databases (4–6)aswell ration efforts focused on improving the annotation of as integrative resources (7,8). WikiPathways has been used metabolism and metabolic pathways by associating to analyze and integrate experimental transcriptomics, pro- unmapped metabolites with database identifiers and teomics, and metabolomics data (9–12). Our previous up- providing more detailed interaction knowledge. Here, date reported over 2300 pathways for 25 different species we report the outcomes of the continued growth and (13) and over the last two years this number has increased curation efforts, such as a doubling of the number by 14% to 2614 pathways, as of September 2017. Through pathway curation and the addition of new pathways, human of annotated metabolite nodes in WikiPathways. Fur- gene coverage present in at least one of our pathways has thermore, we introduce an OpenAPI documentation increased from 30% (7600) to ∼50% (11 532) of all unique of our web services and the FAIR (Findable, Acces- human protein-coding genes, see Figure 1. sible, Interoperable and Reusable) annotation of re- The WikiPathways database is improved by continuous sources to increase the interoperability of the knowl- data curation and updates through an expanding commu- edge encoded in these pathways and experimental nity: 634 individual contributors to date and 2850 edits on 1060 pathways between August 2016 to August 2017. The
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